Doctor Who: The Run that will Never End - Series 1
by minebot
Summary: What if there was a different ending to Hide? An ending which threatened the very essence of humanity, and there is nothing the Doctor can do. Or is there? This is the first of many Series' I will be posting, all based off of this one. Chapter 6 is out now. I will be posting the other chapters eventually. May be a little bit gorish later on.
1. Chapter 1

Hey everyone. This is my first ever fanfiction of anything. Ever.

I had the idea to write this after watching Season 7 episode 9, Hide. I felt the monster was misused, and could've become a more dangerous foe than any of the other monsters. Neil Cross dissapointed me with his ending of the episode, so I rewrote it. It begins with the scene after the Flashback, where the Doctor realises the Monster is just a lovestruck little cuddlepuss. In my version, the Doctor realises something else. Something scary. He is the Doctor, and he is truly Afraid.

Disclaimer Time: I own no rights to Doctor Who. It all belongs to the BBC and Steven Moffat and all the others who work on it.

* * *

"I'm so slow," said the Doctor, "I've always been slow." He turned on his heel, looking at Clara, and straightened his bowtie. "Run"

Clara had no idea what had been going on. Emma had warned her that the Doctor was trouble, that the Doctor would be her mistake. She chose not to listen then, and she sure as hell didn't want to listen to that now. All she could do was run. But this was a different form of running. It wasn't a chase, or an escape. This didn't fill her with adrenaline or with wonder. It filled her with Fear. The worst fear she had ever felt. She saw it in the Doctor's icy stare, something was Wrong.

-Later, inside the TARDIS-

"Doctor, calm down. What's wrong?" Clara asked, her voice quiet as if she was hiding from something. "D…Doctor?" The Doctor took his hands out of his hair, and placed his face in his palms. "I'm sorry Clara. I'm so sorry" and then he chuckled, as if he had a sudden memory. That laugh always scared Clara, the laugh in the middle of the scariest moment of her life. When the man with the impossible chin and the non-existent eyebrows appeared out of nowhere and asked to take her to impossible places, she didn't once think of the dangers. But now they were here, staring her in the face.

The Doctor got up, and started playing with the levers and knobs on the T.A.R.D.I.S control panel. "Doctor. Where are we going?" she asked, not sure if she wanted the answer. "Nowhere," he replied, "We are never leaving this place. Ever." He seemed to get angry now. "I'm deactivating the T.A.R.D.I.S. It's time for me to settle down I guess. I was always scared of this day. But why now, I am still so young." Clara couldn't understand a word he was saying. The Doctor was giving up? Clara had seen the man do much more in a day than any one person could do in a lifetime. He would just fix his bowtie, snap his fingers and POOF. All troubles were gone. And then they'd saunter on to another magical location, get into more trouble and then fix everything. And she loved it. She loved the rush of the Run, and the amazing creatures she had seen. She had seen galaxies grow and die within seconds. She loved that too, but always felt sad. The death of existence, that's what she feared. The Doctor had seen it, so she was always amazed at how cheerful he seemed, but now that had changed.

"Clara," said the Doctor, calmly "Please give me one last minute with her, I have to say goodbye." Clara did as she was ordered, and left the T.A.R.D.I.S, closing the door behind her. The Doctor looked up at the roof of his T.A.R.D.I.S, fearing what was to happen. "Activate T.A.R.D.I.S visual output, choose anyone you'd like." The T.A.R.D.I.S must have felt the pain in the Doctor's heart, and what she did then only added salt to his wounds. She was Susan, his Granddaughter. The one he had abandoned left alone. He took her from the safe haven of Gallifrey, and brought her to Earth. She was forced to change her entire life due to the mistakes of the Doctor. And he remembered everyone who had been changed because of him. He remembered Rose, trapped in a different dimension. He remembered Martha, and the terrors she had faced with her family. He remembered Donna, who would never remember her adventures with him, and her part in saving the universe. He remembered Amy and Rory, who were both taken from their normal lives and thrown into a vortex of turmoil. Now they were gone too. He still had Clara, but for how long. He had seen her die twice now, and he wasn't sure what would happen next. She wasn't normal.

"Yes Doctor?" asked the T.A.R.D.I.S, using Susan's voice. It broke him. He fell to the ground, wiping his eyes constantly. "It's the end, my everlasting companion. We've reached the end of path." "It's never the end, my Doctor, you haven't gotten rid of me yet. I know what is to come, and this isn't the end. You're just about to have a brilliant idea, like you always do, and we will fly off again. " The Doctor got up. Eureka, one might say, and said "That's it." He smiled, kissed the console, wiped the dust from his mouth and made a mental note to clean the console when this ended. If it ended. "T.A.R.D.I.S, I am about to go to my death. Will you let me do this?" "Whatever you think is right, is right my Doctor". The Doctor thought for a second. He knew what he had to do. "Open the visual chat console". The T.A.R.D.I.S did as he commanded, and an image of Clara popped up behind him. "Clara, behind you." She got up, turned around, and saw the Doctor's hologram. "Doctor? Doctor, what's happening? Are we OK?" The Doctor regretted the next thing he did. But he had to do it. For the planet. For the Universe. For all Existence. "Goodbye Clara. We'll meet again. One day". He locked the T.A.R.D.I.S door with his Sonic Screwdriver and pressed a button on the console. He turned just in time to see Clara's face. No words came out of her open mouth, but her eyes said it all. 'Doctor,' her eyes cried, 'why? Why are you leaving me here?' And he knew he had made a mistake, but he kept on going, trying to forget her face. But he never forgot. He never forgot anything.


	2. Chapter 2

Here is chapter two, as promised. This one is mainly Clara orientated, and just sort of explains her life post-Doctor. But what happens when she hears the sounds of the Big Blue Box again? And what if it isn't blue?

Disclaimer Time: I own no rights to Doctor Who. It all belongs to the BBC and Steven Moffat and all the others who work on it.

Note: If there are any grammar or spelling issues, please alert me in the review section rather than complaining about it. Thanks.

* * *

20 Years Later

Clara was waiting, as she did every day. It had been 20 years, yet she still kept faith in the doctor. Emma had disappeared after Alec's death, and Hila Tukurian had perfected her time machine and was off having an adventure. Hila had offered Clara the chance to travel space with her, but Clara only wanted to travel with the doctor. She promised to come back, but it had been 15 years since then. And now Clara was alone, as usual. She felt strange, being 45 and rewitnessing the evolution of Human Society. It felt weird watching Friends, her favourite show which had just premiered at the time, and knowing how it all ended. It was funny watching Bill Clinton and his family on TV, knowing that in 4 years he would admit to cheating. Clara wasn't old, but she wasn't young either.

She never left the Caliburn Household. Not even to visit any nearby towns. Alec Palmer had hired a hand boy before he died, who went and brought groceries from the town. She would go into the forest once or twice every few months, but other than that, she would just sit around the house and watch TV, waiting for the sound of the engine. And there it was.

20 years it had been. 20 years, and not a sign of the Doctor. But Clara didn't care, because she was done waiting. She was ready for the Doctor to whisk her off onto another planet. Of course she would need to get some exercise done, in order of the running. But that could wait till later. Right now the only thing she could do was run outside, to the centre of the forest, where the sound of the T.A.R.D.I.S engine was roaring. It wasn't like what she remembered. It was more of an urgent sound, as if the T.A.R.D.I.S was in pain. But she ran into the forest, getting her hair caught in the branches more times than she would have liked, but it didn't matter. All she cared for was the site of the big blue box. And there it was. Almost.

It wasn't blue, but Red. A dark shade of blood red, and there were huge dents and claw marks along the edges of the box. It was still rematerialising, so Clara had to wait. And wait. And wait. The T.A.R.D.I.S was still going. It was a lot longer than normal. She put her hand out to touch it, and she felt the door. Then it was gone. Then it was back. She pushed as soon as the felt the door again, and the door flung open. And there was the Doctor, tied to the console. "Doctor!" Clara screamed, and jumped into the T.A.R.D.I.S., but it was gone. The rematerialisation didn't work. And she cried. The Doctor left her again.

She waited there, lying in a ball, her tears pouring out. The Doctor had abandoned her again. But there was another sound, another T.A.R.D.I.S noise. But it was louder, as if it was multiple T.A.R.D.I.S's. Or is it T.A.R.D.I? She didn't really have the time think, as the ground began to quake around her. And then, all around her, T.A.R.D.I.S's began to materialise. She counted 13, 13 T.A.R.D.I.S's And as soon as they had finished materialising, all of the doors opened. And there was a different man inside each one.

The first one had an older looking man, with a black hat, and a young girl with him. The next one had somewhat of a bowl cut, and was quite short. The next had white curly locks, and a fancy suit thing. The next one had similarly curly hair, but wore a hat and a scarf. And he had a robot dog. The next one had flat blond hair and a vegetable on his collar. Celery or a leek, she didn't get a good enough look. The next one wore the most ridiculous clothes she had ever seen. The next wore a hat that matched his coat, which had question marks along the collar. He seemed to have an umbrella with him. Next one had curly brown hair as well, and some sort of scarf tie. He had a pocket watch in his hand. The next one was bald, almost, a little bit bald. He wore a leather jacket and black pants. The Tenth one had a trench coat, and a blue suit with a red tie and sneakers. Next was her doctor. The one with the chin and the eyebrows. And when she saw him, she almost burst back into tears. The next T.A.R.D.I.S was exactly like the one she had seen before, red with claw marks. Inside was a man with Slick Black hair that was combed back. He had an insane amount of pockets on his suit. The final one was bald, muscular and had an eye patch. A war veteran he seemed like.

Clara wasn't the smartest person alive, but she was no idiot. It took her a moment to gather her thoughts when she realised who they all where. They where all the Doctor, all different versions of him. But only the last two actually recognised her, not including her Doctor. His eyes were as emotionless as the others towards her. "Clara" they all said in unison. "Clara Oswald, the Girl twice dead. Clara Oswald, you must run. Clara Oswald, beware the dark, beware the light, never stop running. Run until you find yourself, and only then you will know what to do."

And so began Clara's first adventure. The Palmer's had left her their hefty fortune, and a slightly old car, but it was all she needed. She didn't know where to go, or how to get there, but she Ran. And she never stopped, until that one day. The one day where her life changed for the better. When she found the Doctor


	3. Chapter 3

Here is chapter three. This one continues Clara's story, and her attempts at finding the Doctor. The First Series will revolve around Clara, and her quest.

**Disclaimer Time:** I own no rights to Doctor Who. It all belongs to the BBC and Steven Moffat and all the others who work on it.

Note: If there are any grammar or spelling issues, please alert me in the review section rather than complaining about it. Thanks.

* * *

"Captain Morrow. Jenny Morrow. Commander of the Star ship Alaska. Care for a jelly baby?" said the young blond girl in front of Clara. "Uhh… no thanks. My name is Clara Oswald, I heard you can help me find the…" she began, but was interrupted by the girl "The Doctor? Well, you came to the right place. Where did you hear about us?" Jenny asked. "Oh, there was this website online. LINDA United or something like that. Gave me some information on where to find the Doctor and people who can help me find him. For some reason they stopped posting on their site, so I did my own private investigating. Then I found this woman, who helped me find you."

It had been many years now, and Clara was still running. She never stayed in one place long, and never had time to get to know anyone. She kept running, not sure from what, but she never stopped. It was late 2011 now, and Clara felt she was getting closer. In 2005 she met a man named Clive Finch, who gave her some ideas on what she was looking for. Wherever there was trouble, there was the Doctor. He had died of some sort of mannequin attack. She had a short run in with a woman named Sparrow, who ran a shop. She remembered the Sparrow woman, as the woman from the store who gave her number to the man who could solve any problem. She gave her the Doctor's number.

Most of the people she had met were of no use to her. They only repeated what she already knew. They went into more depth of his different forms, or 'regenerations', but that didn't matter to her. She wanted to know where to find him, and then she had a stroke of luck. She was alone at night, wandering the streets, hoping to God for a sign of the Doctor, and then it happened. Two people ran down the streets, both African American, one woman and one man. She noticed their impressive weapons, and decided to follow them. She had learned that running usually meant something was following, and she didn't want to stick around to see what it was.

"Code Alpha Charlie Whiskey, Mickey is he here?" said the woman. She sounded scared, Clara could feel it. "No sign of him. We're on our own here Martha." replied the man. Martha, the name reminded her of someone. Then the next few words were what really changed it for her. "Doctor, where are you. Doctor, we need you." said Martha. And then Clara decided to butt in. It seemed like the two soldiers hadn't noticed her, and too be honest she was surprised they didn't, the way she was panting so loud. It was hard to keep up with them; she hadn't actually run this fast in a long time. "I'm sorry, but did you mention the Doctor?" Clara asked through heavy breaths. The two seemed to jump. "I'm sorry ma'am, but this isn't a place for the elderly. Please allow us to do our jobs." Said the man, when Clara realised, she was 60 years old. 60 years old, but she felt as if she was still 25. But she was determined to find the Doctor, no matter her age. "Listen to me; I need to find the Doctor. He is looking for me, and I need to help him. Please, I beg of you. I've been searching for close to 40 years now. He left me, but I will find him. With or without you." said Clara, in a fit of rage and despair. So through many more links, she found Captain Jenny.

And here she was, 61 years of age, and the closest she had ever been. "So captain, do you know where I can find him?" asked Clara, hoping that this was a victory in her quest. "Maybe not me, but there are many on board who can help us. But before we let you onboard, who was it exactly that helped you find us?" Clara had to rack her brains to try and remember the name, "Martha, I think it was Martha." The name must have been familiar to Jenny, as her face looked shocked. "Ma…Martha. Martha was there when I was born. Uhh, welcome on board Mrs Oswald." Clara felt the need to correct her, but it wasn't important. She wasn't married, she never actually loved anyone. Well, maybe the Doctor, but she wasn't sure about that yet. "Sorry but, what was your name again?" asked Clara. "Jenny, Jenny Morrow. But to be honest, Morrow isn't my real name. I don't know my real name. My father left me before he told me anything about himself, but it wasn't his fault, he thought I was dead." confessed Jenny. "Who was your father?" Clara asked, but she had an idea. "The Doctor," replied Jenny, "but I wasn't born like a normal person. We had this kind of cloning thing, so yeah. I got a bit of his knowledge and stuff, so I made this little group of people with access to Time Travel and what not.

But we realised that people were actually getting lost mid-travel. One of our most recently lost was someone called Hila Tukurian. She was stuck in a pocket universe, but then she was saved by the Doctor. She came back here, but on her trip back to the time she had left from, she disappeared. Another one of our own who have recently been lost was another Doctor. Doctor Brown and his apprentice, Mr McFly. But they were amateurs at this, to say the least. We've cancelled all attempts at travelling, or 'Hopping' as we call it here, except for a Dr River Song. You'll want to talk to her as well, she can be a real help."

Clara made a note to talk to Dr Song, but she was still shocked to have met the daughter of the Doctor. She knew she was in the right place, but she had one question. "You mentioned cloning. Do you still have that machine?" Jenny looked puzzled, she wasn't expecting that. "I think we do, but we tend to stay away from it. Why? Would you like a clone?" Clara had a sudden idea. A clone was what she needed. "Yes please, but is there a way we can reduce the age of it?" Jenny was ready for this one, "Yes. We've upgraded it to be able to be whatever age we choose. Anything else you need to know?" One last question Clara had to ask. This would determine whether her plan would work or not. "Just one last thing," she said, "is there a way I can get me and my clone to switch minds?"


	4. Chapter 4

Here is chapter four, featuring Professor River Song. Clara has finally found a way to renew her younger body, and is on her way to finding the Doctor.

**Disclaimer Time:** I own no rights to Doctor Who. It all belongs to the BBC and Steven Moffat and all the others who work on it.

Note: If there are any grammar or spelling issues, please alert me in the review section rather than complaining about it. Thanks.

* * *

"It's called a Psychograft, or something like that. It's used to switch minds between two subjects. We found it in the ruins of New New York. Which isn't actually real yet, so don't go telling people about it." Clara enjoyed Jenny's warmth and friendliness. She was glad to have found someone who could be of use to her, and someone with the same thought process as the Doctor. "You're sure you want to go through with this?" asked the Captain. Clara just nodded, hoping the next bit wouldn't hurt. She placed her hand inside the machine, and she was wrong. It did hurt. Quite a bit actually. But she kept it in there, waiting for something to happen.

"You can take it out now." said Jenny. Clara did as she was told, and pulled out her hand, grimacing at the scar that was there. "Now what happens?" she asked. And as soon as she said it, a pair of sliding doors opened to reveal a perfect clone of a younger version of Clara. It was amazingly accurate, to the nearest detail. Clara almost forgot how to breathe, she was so dumbstruck. It had been many years since she had seen anything unearthly, so what had just happened felt like a field trip through all of her wildest dreams.

"Strap her up to the machine boys," asked Jenny, as a pair of soldiers picked up the clone and strapped her into a seat. Clara had taken her seat next to the clone. They both had helmets placed on them, as if it was something out of a movie. "You realise the risks, right? This is a piece of future tech; however it has been remade out of scrap parts. It's nowhere near as stable as it was once." Clara knew this, so she nodded and said, "When we are done with this, please bury her. I want to know that I am taken care of. You are sure she hasn't had the time to grow a mind yet, yes?" Jenny nodded unsurely in reply. "Oh God," Clara thought, "This isn't going to be pretty." And guess what? Clara was right. It was a horrible feeling, sitting in the chair, as she felt waves of energy flowing through her. She could literally feel her soul being pulled out of her and being placed into the new clone. And then it stopped. She stopped hurting, and looked around. Her eyes needed a while to adjust, and she realised that they had never been used before. She looked to her right, and then to her left, where she saw herself.

It was a weird feeling, seeing herself but 40 years older. She would never get used to it. She fell to the ground as soon as she stood up; her new legs weren't fully functional yet. But she eventually got used to that as well. "Clara. Clara can you hear me?" Jenny said, looking worried. "Yeah, yeah I'm fine," replied Clara, "can someone help me get up?"

10 Days Later

It had been 10 days, and Clara had finally gotten used to the new body. She had to do countless hours of Physiotherapy to get her motor skills functioning, and her legs were kept straight by a pair of leg braces, which were gone now. She was ready to begin the next leg of her journey. Dr River Song.

River Song was an older looking woman, but not as old as Clara had been not more than a fortnight ago. She had curly brown locks, and wore a sweater. She wore a lot of sweaters, Clara was told. Clara entered her office, and noticed a few things. The first was a blue diary on Dr Song's desk, which looked a lot like the T.A.R.D.I.S door. Then she noticed all the archaeology certificates and Diplomas River had placed on her walls. Dr Song herself was seated on a chair behind a desk, wiping her eyes. When Clara knocked on the metal door, River looked up and Clara saw her tear streaked face.

"I'm, I'm sorry Dr. I didn't mean to disturb. Is this a bad time?" asked Clara. "No no Clara, it's ok. Come in. And it's Professor Song, not Dr Song. I don't deserve that title." Clara was unsure about entering, as Professor Song cleaned her face and put on a smile, which was obviously faked, but Clara tried not to notice. "How can I help you?" Clara wasn't sure what to say. "Jenny told me you could help me find the Doctor?" as soon as she mentioned the Doctor, she saw River begin to get emotional again. She wondered what River and The Doctor had in common, but she decided not to ask. "Ah, the Doctor. The man who can change someone's life by putting out his hand. The man who changed my life, and showed me the furthest points of life. The man who hasn't come home in ages, and has left me alone. I did some research on you Clara, and I believe the Doctor did the same to you. So why do you still look for him?"

Clara was still not sure what to say, but she came up with something, "Because he promised me he'd come back, and it is my duty to find him." River chuckled. "Duty? What do you mean by duty? The Doctor has been missing to you for about 40 years, but for the rest of the universe, the Doctor has not been seen for 100's upon 1000's of years. Out of the entire universe, why is it you who has to find him? Me, Jenny, everyone aboard this ship; we are all looking for him. But let me be honest Clara, we have given up hope. Why are you the one who was _chosen_ to find the Doctor?" River said with another forced smile. Clara felt like she was being scolded, "Because the Doctor told me to. And not just my Doctor, 13 Doctors. They all told me to find him. And I will find him, with or without your help," Clara said with a hidden smirk. She had never been so confident or authoritative before, so she continued, "Do you really care for the Doctor? If so, then you can never give up on him. And if you've given up on him, then you are of no use to me." Clara stormed out of the office. She liked her new found strength, and kept walking until River said, "Wait Clara! I'm sorry, please come back. I haven't given up on the Doctor, not just yet. But our search for him isn't going anywhere. I don't know how much longer we can keep all these soldiers and Hoppers here, without the Doctor to boost their morale."

Clara had to agree, she had been waiting for the Doctor for 40 years, but if these people had actually accessed the power to travel time, they may have been waiting for a lot longer than her. If they had been able to keep their faith in the Doctor for so long, then she knew these were the people she was looking for. With a new body and a new faith in her heart, Clara was ready to find the Doctor. No matter what it took.


	5. Chapter 5

Chapter 5! Sorry it took so long to write, I had a case of writer's block. Clara is ready for her first adventure with Jenny, but finding the Doctor wasn't how she expected it to be.

The story becomes slightly darker now. The rest of the story will be quite dark. Due to complaints by a friend of mine, I will write two stories. One dark (this one) and one that has a cutesy ending like normal Doctor Who episodes.

**Disclaimer Time:** I own no rights to Doctor Who. It all belongs to the BBC and Steven Moffat and all the others who work on it.

Note: If there are any grammar or spelling issues, please alert me in the review section rather than complaining about it. Thanks.

* * *

Clara, equipped with a new body, was ready to begin her training. After her conversation with Professor Song, Clara asked to learn the secrets of Hopping, in order to find the Doctor. Professor Song had instructed Jenny to mentor Clara, and so began her training.

At first Clara had trouble getting her head around the idea of Time-Travel. The first lesson was how time worked, not how to travel through it. Jenny did her best to teach Clara, but all she understood was that Time was like a ball of wibbly-wobbly timey-wimey…stuff. It didn't make sense to her.

"Time isn't a linear progression of cause and effect" said Jenny, slowing down so Clara could make her notes. In all honesty, Clara made no attempt to learn the science of Time, and wrote down what Jenny said, regardless of whether or not she actually understood it.

She was scheduled to do a week of Time Sciences, but due to her general lack of understanding, it drew on for a month, before she finally got the jist of the whole time travel science. Finally, River allowed Clara to begin her actual training.

"Here Clara," said River, giving Clara a large bracelet with an interface on it, "it's called a Vortex Manipulator. They aren't easy to make, so don't try and put yourself in as much danger as you can. Only you and I have these, so don't let the other hoppers know."

Clara looked up at River, seeing a glimpse of hope in her eyes. Jenny had told her stories of Clara, of her mother and her travels with the Doctor. River was a stronger woman than Clara had seen that night, many months ago. "Thank you, River. Thank you so much." Clara hugged the older woman.

River returned the hug, "Before you leave, it is recommended you take someone with you. All time travellers need their companions. My post is here, so I suggest Jenny or one of her hoppers." Clara had already decided to ask Jenny to come with her, so she knew what to do next.

After a short conversation and little-to-no hesitation, Jenny was prepared to go on her adventure with Clara. They said their goodbyes to all of her trainers and teachers, and to River. Clara found it the hardest to leave River. She knew River was a strong, independent woman, but the weakness she had seen so many weeks ago made her wonder if River could be left alone.

"Be safe Clara. And if you find the Doctor," A sad smile grew on her lips, "smack him as hard as you can for me. And then tell him I am still waiting. Always and forever." And then she was gone, back into her quarters.

"Where to first, Captain?" asked Jenny. Clara didn't know how to reply. She had all of time and space to travel to, and she was in charge, but she hadn't seen everywhere yet, so she couldn't decide like the Doctor could. But she had one idea. "I have a feeling I know where we should go. Ready for an adventure?" Jenny nodded, and Clara grabbed her hand. She set her Vortex Manipulator to the co-ordinates she planned to visit.

1974

Clara and Jenny appeared in a forest, outside of a dark house. They heard banging on wood, and Jenny looked startled. This was her first experience at proper time-travel, and she felt spectacular. Clara looked a lot less excited, she recognised that banging sound. It was her, banging on the TARDIS door. Crying for the Doctor to open the door and let her in.

"Clara. is that…is that you?" Jenny asked, pointing at a crying figure standing mere metres away. "Ignore her Jenny, we can't cross the timelines. You know the rules." Clara wanted to go and grab the figure. To hug her, and tell her that life was going to get better. "We need to get inside the TARDIS."

"TARDIS?" asked Jenny. Clara felt a bit surprised that Jenny didn't recognise the name. "It's the Doctor's time travelling machine. It looks like a police box from the 60's or something, but it's just a disguise. It's the most amazing thing I've ever seen, but it always feels so empty. Like it's missing something, it's cold. Too cold. And it hated me, probably still does, but I don't care about that." Clara said, while typing in a few new co-ordinates.

WOOSH. The next second, they were inside the TARDIS, staring at the Doctor. "Clara, we did it. We found him. Doctor, Doctor it's me! Jenny!" shouted a thrilled Jenny. Clara understood how Jenny felt, the Doctor being her father and all. She'd do anything to see her mother again, but it was too late for that. She had found the Doctor, and that was all that mattered. She knew she must have had the stupidest grin on her face at the moment, but it suddenly faded when she saw the Doctor.

"Get out! Get out at once! Clara, what have you done? Get back and stay away!" shouted the Doctor at Clara and Jenny. The darkness in his eyes scared Clara, and she ran backwards, deeper into the TARDIS. Jenny followed closely. "No Clara, Not in there! You brought this upon yourself!" Clara heard a voice shouting behind her. She wondered what had happened to the Doctor to have him turn so mad. She felt a tear grow in her eye, she never expected her Doctor to become a man like this.

"Clara, what happened? Why is the Doctor so mad? What's happened?" asked Jenny, as they kept running. She heard a footstep coming behind them, the Doctor was chasing them. A part of her wanted to stop, and let the Doctor catch them. Just to see him again, just to hear his voice. His proper voice. But she kept running, not knowing why. It just felt like the right thing to do, because this was not her Doctor. This was a demon in Doctor's clothing.

"Clara, come back! Stop running! Don't go too far into the TARDIS" shouted the Doctor. But Clara kept running, for what felt like hours. "In here, Clara, in here!" shouted Jenny. She had found a room, albeit a very dark room, but a place to hide from the Doctor nonetheless.

When she heard the Doctor run past the room, she let out a breath she didn't realise she was holding. "Where are we?" whispered Jenny. The room felt cold and eerie, like everything dark and horrid was locked in here. Clara felt all her childhood fears return to her in an instant, and then fade as lights came on in the room. But she wished it had stayed off.

What she saw was horrifying. In the centre of the room, tied in chains with many wires running through it, was a woman. A young woman of around 13 she looked like. She wore a skirt and a sweater, and had her head running low. The girl looked up at Clara and began to scream.

"Sleep now Susan, sleep. Ignore these women." Clara heard a voice behind her, and a hand fell on her shoulder. She looked up and saw the man who was once the Doctor, staring at her. There was still darkness in his eyes.


	6. Chapter 6

Whats this? TRTWNE Chapter 6 is out? No way!

Sorry it took so long, had no idea what the hell I was doing, but now i'm back.

This chapter reveals the series' main villain, a remake of the Hide monster. Sorry it is a lot shorter than normal (about half as long), but I just put this out as a filler till the next part. Thanks.

**Disclaimer Time:** I own no rights to Doctor Who. It all belongs to the BBC and Steven Moffat and all the others who work on it.

Note: If there are any grammar or spelling issues, please alert me in the review section rather than complaining about it. Thanks.

* * *

"Doctor. What is it?" asked Clara, staring shocked at the body hanging from the ceiling, wired in and out by a number of pipes. Its eyes were staring at her, empty pupils, but Clara could feel it staring at her.

"It? IT?! This is no "it", not an object you disgusting humans can objectify. This is my granddaughter, Susan. Or Akhrytior. Unfortunately, she grew too close to her human name. Sickening really, sentimentality from a name, loving a lie." The Dark Doctor grimaced and walked towards the mesh of girl and machine and held her under her chin.

"Destroyer of Worlds. Killer of Species. And yet, he loves? Not just that. He loves humans, he loves hybrids, he loves everything. The man, who was destined to bring the universe to its end, ends up falling in love with it. Foolish Doctor, two hearts are two too many for a bloodthirsty devil."

Clara couldn't understand what the Doctor was saying. Or if it was the Doctor who was speaking. She just couldn't get her head around the current situation. She wanted to leave, run away, use the manipulator to escape. But she couldn't. She wasn't sure if it was fear keeping her there, or some trick by the Dark Doctor.

"Who are you? Who are you honestly?" asked Jenny, who still had the fire in her heart to be able to confront the beast-in-Doctor's-clothing. And then he turned around, with the sweet eyes of the real Doctor and the slightest smile on his lips.  
"Clara, it's me. Honestly. No need to be scared." Clara's mind was bent on not trusting the man in front of her, but her heart disagreed. She ran towards the man, and hugged him tightly, tears streaming from her eyes.

"Oh Doctor, I… I was so scared. What's happening Doctor?" asked Clara, through closed eyes, streaming into the Doctor's jacket. "Compassion, my dearest Clara. A Human's greatest weakness."

Before Clara knew what was happening, the Doctor was staring into her eyes, and she could feel her soul leaving, exiting through the eyes. "They say," said the Doctor, "that the true soul of a Human is reflected in their eyes. You know not how true you are." The Dark Doctor had returned, laughing while Clara felt herself leaving her body.

ZAAP

The Doctor was on the floor, covering his face. Clara had fallen with the Doctor but got up before him. She turned towards the origins of the blast, and saw Jenny, helping Susan out of her wires. Susan had a wire in her hand, steaming at the end. Clara looked back at the Doctor, and walked backwards towards Susan and Jenny.

He stood up, and dropped his hand. And it definitely was not the Doctor. Half of the man's face was that of the Doctors, except it had a shade of rage on it that Clara had never seen before. The other half was a mangle of wood and bone. A set of teeth which looked to be made of marble, and a single black eye, which filled Clara with a fear she had never felt before. She recognized this beast though. He was there in the pocket universe; she had seen Hila's pictures of it.

"Worthless little Humans. Do you think you can stop me? Your precious Doctor tried to stop me, and look what happened to him. I wear him like a jacket, the last Timelord. He made a mistake, trying to find me." The beast man laughed. Clara found it hard to believe that this Beast had bested the Doctor, and yet she could believe nothing else. The Doctor was dead, if this Beast was true.

"No. No. You didn't…you couldn't…oh god, oh Doctor." Clara fell to her knees, but tears wouldn't come out. She was done crying, it was time to fight. She knew it, and so did Jenny, and the Dark Doctor.

"Where is he?" asked Jenny. The Beast laughed. "I told you, girl, I killed him. I ripped his insides out, and replaced it with me."

"No, where is he actually? I feel the Doctor, always have. If he's dead, I would feel it. But he isn't, because I still feel him. Crying out to me." The Monster lost its grin. "Smart girl. Yes, the Doctor still _exists, _however, you won't be able to find him."

"Why not?" asked Clara.

The Beast smiled. "Because Girl," he said, "you can't find someone if you are dead."

And then he charged at them.


	7. Chapter 7

Here is Chapter 7. Its longer than the last one, and reunites Clara with the Doctor.

The Doctor is dead, but still exists. What does this mean, and will Clara be able to find her Doctor before it is too late?

**Disclaimer Time:** I own no rights to Doctor Who. It all belongs to the BBC and Steven Moffat and all the others who work on it.

Note: If there are any grammar or spelling issues, please alert me in the review section rather than complaining about it. Thanks.

* * *

The beast charged at Clara, keeping its wooden arm in front. All that was left of the Doctor on the beast was half of a face and one arm. It was a sickening seen, a scene that hit Clara with so much mental force that she didn't have the energy to be scared. Too scared to be scared, she thought to herself.

Blast after Blast, Jenny and Susan were aiming (albeit sloppily) and attacking the beast. He was never fast enough to hit Clara, but he always managed to slither past the lasers heading towards him.

"No use in running girl, I am going to kill you." The Monster laughed as he chased Clara around the room. The door was locked, so she couldn't leave. Two more blasts, and the Monster had frozen. He was stunned.

Clara didn't take the time to allow herself to catch her breath; she knew he would reactivate soon enough. She got around to Jenny, using her as a meat shield in the case that the beast awoke. And then it did.

Except this time it didn't charge for her, but leapt from one side of the Room onto the other, breaking a hole in the wall and going through. Clara went to observe, but was held back by the half-human-half-machine named Susan.

"No" it tried to say, but there wasn't enough of a mouth left to create the word. She reached out into the hole, and instantly pulled her hand back in. Except it had aged, possibly a few decades. Clara thought she spied a smile grow on Susan's face, but she couldn't tell. Until the regeneration began.

Susan's aged arm began to glow, shooting out a blast of yellow light. Clara went to touch the hand, and as she was touched by the light, all of her battle damage healed. All of a sudden the rest of her began to glow too, and eventually Susan had re-grown her missing skin.

"OH. MY. GOD." Were the first words to escape the newly fixed girl. She seemed to be a young teenager; however the sight Clara had just witnessed forced her to believe that Susan was a Timelord. That, and the fact that she was claimed to be the Doctor's Granddaughter.

"Oh, thankyouthankyouthankyouthankyou!" exclaimed the girl. She stretched out her limbs, as if she had just woken up. "Oh god, it's good to be whole again." She said with a warm smile.

"Alright, now that it is gone, let's go find the Doctor?" suggested Clara. She didn't spy the puzzled look on Jenny's face; as she was too busy watching the hole in the wall heal itself.

"How do we do that?" asked Jenny.

"I've seen the Doctor talk to the TARDIS before, so I guess we can ask the TARDIS where to find the Doctor." Replied Clara. She knew what she was doing.

BACK IN THE CONTROL ROOM

"Umm, ok. TARDIS, do you hear me?" asked Clara. A whirring sound escaped the TARDIS console. She took it as a 'Yes'.

"Find the Doctor please," asked Clara, smiling, thinking she had finally gotten the answer she wanted. She could finally find the Doctor, the REAL Doctor. But then the smile faded.

"No records of 'The Doctor'" replied the console, "'The Doctor' is not a valid reference."

Meanwhile, in Dubai, 2013

"I swear to God, I saw them. The aliens, I know I saw them!" said a man with a giant chin.

"I'm sorry Mr. Smith, but we can't go to the government with claims of Aliens. Please go home, we've had enough of you." Replied the Woman at the counter, she had a worried look on her face.

"Please, you have to hear me. I've seen them; I know I've seen them." John Smith exclaimed.

John Smith was an average man, with a chin so big it could pick up a truck and almost non-existent eyebrows. He always wore a bowtie, and he had an unhealthy addiction to Science Fiction. Novels, Movies, Television, Comics, etc. You name it, he's seen it.

John Smith was known around Dubai as being the creep who saw the Aliens. He was always posting on online forums about his experience with Aliens, about the presence of aliens on the internet. It was even believed that the Internet Meme "Aliens" was created by him, after watching every episode of 'Ancient Aliens'.

John Smith lived a boring life, no job however he always had money. He took Spanish classes at a local college, as a hobby in between his alien hunting. He had invested in many different models of telescope, and had tried many times to hack into the Hubble telescope.

Little did John Smith know that he had once lived the life of an Alien Time-Traveler, who had explored the cosmos he had only dreamed of. John Smith often dreamt about his adventures as a time-travelling alien, always with a lady by his side. Sometimes he had different faces, but he mainly kept his own face.

And little did John Smith know that his adventures would come back for him.

That night John Smith was going out for pasta at a nearby Italian restaurant with a lady he had met at Spanish. He was hoping to go steady, as she had a nice personality and was all around HOT. He had just finished uploading a picture of his dinner on to Instagram as his date returned to the table.

"So John, what is it that you do in your spare time?" she asked.

John had no idea how to respond. People normally didn't like to discuss aliens and the end of mankind. "I'm an astrologist. I love looking at space." He thought up on the spot.

"Ah, a Star Gazer." She replied, looking slightly disappointed, "pardon me. I need to use the restroom." She stood up and walked away slightly faster than a normal person would. Two hours later, she still hadn't returned.

On his way home, the man with the Hipster Glasses and the Bowtie looked up to the stars. He always looked up when he felt down, or when he was happy, or hungry, or scared. He just looked up for any reason. He felt safer looking up, except for this night.

He immediately took out his iPhone and photographed the meteor heading straight at him. He just had enough time to get out of the way before he would have been crushed.

He went to look at the meteor, but it wasn't normal. It was not a space rock, but a blue wooden box, with scratches along the side. The doors of the box flung open, and three women stepped out. The one who got out first, a girl with a red handbag and brown hair, smiled when she saw him. She walked up towards him, placed one hand on his shoulder, and slapped him with the other one.

"You stupid little….ugggh. We finally found you. How many freaking John Smith's are there in the universe. You need to put a Space Time locator chip on your clothes so the TARDIS can find you." Said the Girl. She had slapped him quite hard, and he had fallen to the floor. The other two girls picked him up, and took him into the box.

It was bigger on the inside.

"What…what the hell is this? Oh God, I was right! Aliens are real! You are aliens, yeah?" asked the man, photographing every aspect of the Space Box.

"Doctor, Doctor what are you doing?" asked the Blond girl. She was also Hot.

"Doctor," asked John Smith, "Doctor Who?"


	8. Chapter 8

Chapter 8 is here. Clara takes the Doctor (well, John Smith) on an adventure to regain his memory.

The Doctor has no memory of his past adventures, or of Clara. Can she bring him back before the beast returns?

**Disclaimer Time:** I own no rights to Doctor Who. It all belongs to the BBC and Steven Moffat and all the others who work on it.

Note: If there are any grammar or spelling issues, please alert me in the review section rather than complaining about it. Thanks.

* * *

"The Doctor," remarked John Smith, "I'm the Doctor?"

"Yes!" exclaimed Clara, for about the 15th Time. "You are the bloody Doctor, now try to gain your memory back."

"What kind of Doctor?" asked the amazed man who had taken the Doctor's body. "Science or Medicine? Or Engineering? Oh, or Astronomy?"

Clara and Jenny shared an annoyed glance, and Clara slapped him. "Please Doctor, try to remember."

"But that's just it, there is nothing to remember. I am not this Doctor bloke you're on about. Now can you return me home before Matilda leaves me."

"Matilda? Whos Matilda?"

"Matilda is my..." he straightened his bowtie, "girlfriend."

Clara burst out in laughter. All the stress had reached her head and this shocking revelation threw her off the edge. "I suppose you want us to bring her along as well?"

"Whe...where are we going?"

Jenny approached. "All of time and space. Every star, every planet. Everywhere and Everywhen. Until your memory comes back, adventures galore."

"Oh. That sounds lovely." said John Smith, edging closer to Jenny. "I'm glad you are here for me." he puckered his lips and went in.

FATACK!

He was flat on his face. A red face Jenny shot a river of expletives and ugghs from her mouth. Some that Clara had never heard.

"I'm sorry, i'm sorry. I thought you were coming on to me."

"You sick pervert, i'm your daughter!"

"That can't be, me and Matilda are still on first base."

"You don't understand. You'll never understand. Clara, its hopeless."

But Clara didn't listen. Because she was planning their first adventure. But first of all, she needed Jenny.

At the moment, Jenny was sleeping. Regeneration took a lot out of her, and she had admitted to only being a part timelord, so it took more energy to regrow dead cells. Clara did not want to wake her, as she was scared that Jenny would be too fatigued to help them. So she waited before revealing her idea.

"So, Cara," asked John Smith, "where are we going?"

"It's Clara. And we aren't ready to go yet, not until Jenny is ready."

"Well then, can I ask you some questions?"

"Yes, ask away. Make sure its relevant though."

"Well, who is the Doctor? What does he do?"

Clara had to think for a second. "The Doctor is... well, noone knows who he is. That's his secret, his identity. He'll never tell anyone. Except for one person, his wife. What he does? Well, he saves us. And by us, I don't mean us 4, or us humans. I mean us lifeforms. All lifeforms. All planets and stars and people and species. Anyplace anytime, he doesn't ever stop running. He gave me this advice before he left. He told me to never stop running. Well, a few other Doctors did."

"Other Doctors? Are there more?"

"Well, you could say that. The Doctor can regenerate, get a new face and new body if the old one is dying. My Doctor was the Eleventh out of a total of 13."

"Holy mother of God. That is freakin incredible. Wish I could do that."

"You can. YOU are the Doctor. It may be hard to believe, but you are the man who has and will save the universe."

"Sure sure."

John Smith didn't believe that this situation was real. He had actually looked around for hidden cameras, but couldn't find them anywhere. He wanted to explore this Magical Time Box, but Clara had forbade him. Or forbid him. Or forbidden him. He needed a thesaurus. Or just any book. When he was not talking, the Box was a lot more boring than it should have been.

John Smith had always dreamed of Aliens. Having just been told that he was one seemed like it should excite him, but it didn't. He honestly didn't enjoy this current scenario. Well, besides all of the girls.

And then, there was a rapping at the door.

"I'll get it." said John Smith. Hoping it was someone to tell him that he had been Punk'd. But Clara stopped him.

"We are in the middle of the Time Vortex. Who do you think it is?"

"Wait, we are moving? For reals?"

"Oh yes."

Jenny had returned to the console room, when she heard the knocking on the door.

"Its him," said Jenny, "I know its him. Who else could it be?"

and Clara agreed with her, but why hadn't he broken in.

And as if the universe had read her thoughts, a hole tore in the side of the Tardis. The console made a noise, like as if it was in pain. A terrible pain.

A wooden claw reached into the TARDIS room, and grabbed at John Smith, who replied with a girlish scream.

"Emotion is the weakness which clouds Humanity." said the Beast. Clara couldn't see his face, just his arm. "Emotions will kill us all. Just like this man. You can not find the Doctor, because he DOESN'T exist. Give up your hunt."

A snap was heard, and John Smith dropped to the floor. The TARDIS's scream grew louder, and the hole tried to close itself. But not fast enough. The beast was slicing at it as fast as it was regrowing, in a balanced motion of death and rebirth.

Clara ran to Mr Smith. He had snapped his neck, and Clara wanted to cry, but she didn't. Because something was happening. Something which she loved and hated and wanted.

"Clara," began Jenny.

"I know," replied Clara, "He's regenerating."

and the Beast entered the TARDIS.


End file.
